R package implementing Bayesian NMF using various models and prior structures.
-
Updated
Jun 12, 2024 - R
R package implementing Bayesian NMF using various models and prior structures.
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
Detecting mutational signatures via bayesian inference and a reference catalog
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…
Sigflow: Streamline Analysis Workflows for Mutational Signatures, https://github.com/ShixiangWang/sigflow/pkgs/container/sigflow
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Gonçalves JP
Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.
An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use o…
Some workflows I wrote for my phd projects
Shiny server for analyzing mutational signature data; uses mSigAct, ICAMS, and related functionality.
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Python library and package for mutational analysis
B-Cell Lymphomas Mutational Signatures
This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.
Add a description, image, and links to the mutational-signatures topic page so that developers can more easily learn about it.
To associate your repository with the mutational-signatures topic, visit your repo's landing page and select "manage topics."